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Large-scale heavy metal contamination of the upper Clark Fork River from mining deposits has created significant damage to aquatic habitat in the drainage. Trout are present in the system, although with abundances lower than expected. The objectives of this study were to identify critical habitat areas and to identify conditions that continue to limit both native and nonnative trout populations, with the focus of the study on the lingering environmental effects caused by high heavy metal concentrations. A radiotelemetry study, with 256 tagged brown trout Salmo trutta, westslope cutthroat trout Oncorhynchus clarkii lewisi, and cutthroat/rainbow hybrid trout, was conducted from 2009 to 2011. The radiotelemetry relocation data was used to determine temporal and spatial patterns in movement and survival rates in relation to heavy metals and other environmental factors, and to identify critical habitat areas (e.g., spawning locations and overwintering areas). Brown trout spawning occurred in numerous tributaries throughout the basin and in the upper reaches of the mainstem. Cutthroat trout spawned only in tributaries, and these tributaries were often smaller and more degraded by land use practices than brown trout spawning tributaries. Multistate mark-recapture survival analysis estimated that survival is lowest in the stream segment with the greatest amount of heavy metal contamination; the weekly likelihood of survival was estimated at 0.97 (95% confidence interval 0.97 - 0.98) for brown trout and 0.90 (95% confidence interval 0.84 - 0.97) for cutthroat trout. Additionally, weekly survival estimates for cutthroat trout in tributaries was also low (0.92; 95% confidence interval 0.87 - 0.94), likely because of anthropogenic land use pressures. Very limited movement was observed, except in relation to spawning migrations. Cutthroat trout moved greater distances and at a higher rate than brown trout. The results from this study indicate that the remaining mining contamination continues to reduce trout survival rates throughout the basin and should be removed in order to increase trout densities. Additionally, restoration priority should be placed on tributaries that are negatively affected by land use pressures.